mykrobe
Tags: bacteria reads antimicrobial-resistance genotype-prediction sample-scope
Predict antibiotic resistance from sequence reads.
This subworkflow uses Mykrobe to predict antibiotic resistance directly from sequencing reads. It provides rapid genotype-based resistance predictions for specific bacterial species.
Uses explicit positional record fields for reads:
- Input: record(meta, r1, r2, se, lr) where each read slot is Path?
Take
reads: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
r1 | Illumina R1 reads (paired-end) |
r2 | Illumina R2 reads (paired-end) |
se | Single-end Illumina reads |
lr | Long reads (ONT/PacBio) |
mykrobe_species: String
| Name | Type | Description |
|---|---|---|
mykrobe_species | String | Target bacterial species for resistance prediction (e.g., "staphylococcus_aureus", "mycobacterium_tuberculosis", or "enterococcus_faecium"). |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
| Output | Description |
|---|---|
csv | AMR predictions in machine-readable CSV format |
json | Detailed AMR prediction results in JSON format |
run_outputs
| Output | Description |
|---|---|
csv | Merged AMR predictions from all samples |
Module Composition
This subworkflow calls the following modules:
- mykrobe_predict - Predict Antimicrobial Resistance (AMR) for supported bacterial species.
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
Used By
This subworkflow is used by the following workflows:
- mykrobe - Antimicrobial resistance detection for specific bacterial species.
Citations
If you use this in your analysis, please cite the following.
-
Bactopia
Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020) -
Mykrobe
Hunt M, Bradley P, Lapierre SG, Heys S, Thomsit M, Hall MB, Malone KM, Wintringer P, Walker TM, Cirillo DM, Comas I, Farhat MR, Fowler P, Gardy J, Ismail N, Kohl TA, Mathys V, Merker M, Niemann S, Omar SV, Sintchenko V, Smith G, Supply P, Tahseen S, Wilcox M, Arandjelovic I, Peto TEA, Crook, DW, Iqbal Z Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe Wellcome Open Research 4, 191. (2019)